The overall goal of this project is to establish the first successful comprehensive genotyping system to clearly distinguish at the genetic level individual, drug resistant and virulent isolates of the flagellated protozoan parasite Trichomonas vaginalis for future epidemiological and biochemical studies of pathogenesis, virulence and drug resistance. The genotyping system will also be applied to linkage studies, mapping the genome, and determining variability among genomes including the detection of drug resistant, pathogenic and virulent strains. Trichomoniasis is the most common, sexually transmitted infection. Symptoms include virginities and acute inflammatory disease of the genital mucosa, and infections have been associated with pre-term delivery, low birth weight and increased infant mortality, as well as predisposing to HIV/AIDS and cervical cancer. Trichomoniasis has the highest prevalence and incidence of any STI, and its eradication may well be the single most cost-effective step in HIV incidence reduction. This proposal utilises pulsed field gel electrophoresis of very large chromosomal DNA segments cleaved by restriction endonucleases of the Trichomonas genome, combined with gene hybridization, to generate a genotyping system, which distinguishes individual isolates. Such an analysis has not previously been achieved due to extensive endogenous nuclease activity. The genotyping system will be coupled to in situ hybridization of whole chromosomes and electrophoretic karyotyping for gene linkage studies, mapping genome organization and structure, determining genome variability among isolates, and defining markers for virulence and drug resistance.